HEADER GENE REGULATION 01-NOV-18 6IP0 TITLE CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA JMJ13 CATALYTIC DOMAIN IN TITLE 2 COMPLEX WITH AKG COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION FACTOR JUMONJI (JMJ) FAMILY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 90-578; COMPND 5 SYNONYM: JMJ13 CATALYTIC DOMAIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PSUMO KEYWDS ARABIDOPSIS, HISTONE MODIFICATION, FLOWERING, EPIGENETICS, H3K27ME3, KEYWDS 2 GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR H.HU,J.DU REVDAT 2 27-MAR-24 6IP0 1 REMARK REVDAT 1 10-APR-19 6IP0 0 JRNL AUTH S.ZHENG,H.HU,H.REN,Z.YANG,Q.QIU,W.QI,X.LIU,X.CHEN,X.CUI, JRNL AUTH 2 S.LI,B.ZHOU,D.SUN,X.CAO,J.DU JRNL TITL THE ARABIDOPSIS H3K27ME3 DEMETHYLASE JUMONJI 13 IS A JRNL TITL 2 TEMPERATURE AND PHOTOPERIOD DEPENDENT FLOWERING REPRESSOR. JRNL REF NAT COMMUN V. 10 1303 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 30899015 JRNL DOI 10.1038/S41467-019-09310-X REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 45790 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.190 REMARK 3 FREE R VALUE TEST SET COUNT : 2377 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 49.6521 - 6.1608 1.00 2825 146 0.1846 0.1987 REMARK 3 2 6.1608 - 4.8914 1.00 2622 164 0.1892 0.1874 REMARK 3 3 4.8914 - 4.2735 1.00 2624 123 0.1482 0.1653 REMARK 3 4 4.2735 - 3.8829 1.00 2578 145 0.1603 0.1590 REMARK 3 5 3.8829 - 3.6047 1.00 2544 144 0.1922 0.2288 REMARK 3 6 3.6047 - 3.3922 1.00 2557 136 0.1980 0.2071 REMARK 3 7 3.3922 - 3.2224 1.00 2558 133 0.2086 0.2758 REMARK 3 8 3.2224 - 3.0821 1.00 2520 146 0.2129 0.2194 REMARK 3 9 3.0821 - 2.9635 1.00 2523 151 0.2258 0.2941 REMARK 3 10 2.9635 - 2.8612 1.00 2516 144 0.2174 0.2108 REMARK 3 11 2.8612 - 2.7718 1.00 2531 127 0.2182 0.2310 REMARK 3 12 2.7718 - 2.6925 1.00 2513 138 0.2163 0.2758 REMARK 3 13 2.6925 - 2.6217 1.00 2509 132 0.2084 0.2405 REMARK 3 14 2.6217 - 2.5577 1.00 2509 137 0.2187 0.2807 REMARK 3 15 2.5577 - 2.4996 1.00 2486 140 0.2193 0.2472 REMARK 3 16 2.4996 - 2.4464 1.00 2504 132 0.2458 0.2822 REMARK 3 17 2.4464 - 2.3974 1.00 2494 139 0.2669 0.3099 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 3901 REMARK 3 ANGLE : 0.960 5294 REMARK 3 CHIRALITY : 0.065 566 REMARK 3 PLANARITY : 0.007 665 REMARK 3 DIHEDRAL : 22.501 1406 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 93 THROUGH 317 ) REMARK 3 ORIGIN FOR THE GROUP (A): 41.9634 45.0131 142.9468 REMARK 3 T TENSOR REMARK 3 T11: 0.5325 T22: 0.3249 REMARK 3 T33: 0.4498 T12: 0.1987 REMARK 3 T13: -0.0112 T23: 0.0112 REMARK 3 L TENSOR REMARK 3 L11: 1.1705 L22: 2.5801 REMARK 3 L33: 1.7292 L12: -0.8057 REMARK 3 L13: -0.3701 L23: 0.7077 REMARK 3 S TENSOR REMARK 3 S11: -0.0746 S12: -0.1537 S13: 0.0251 REMARK 3 S21: 0.1085 S22: 0.0435 S23: -0.0955 REMARK 3 S31: 0.1001 S32: 0.1158 S33: 0.0196 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 318 THROUGH 484 ) REMARK 3 ORIGIN FOR THE GROUP (A): 53.9034 35.8479 129.9768 REMARK 3 T TENSOR REMARK 3 T11: 0.6367 T22: 0.3344 REMARK 3 T33: 0.4447 T12: 0.1668 REMARK 3 T13: 0.0525 T23: 0.0427 REMARK 3 L TENSOR REMARK 3 L11: 1.2305 L22: 4.5547 REMARK 3 L33: 0.9530 L12: -2.1505 REMARK 3 L13: -0.9220 L23: 1.6179 REMARK 3 S TENSOR REMARK 3 S11: 0.0542 S12: -0.0216 S13: 0.2446 REMARK 3 S21: -0.4091 S22: 0.0168 S23: -0.3591 REMARK 3 S31: -0.0921 S32: 0.0270 S33: -0.0717 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 485 THROUGH 564 ) REMARK 3 ORIGIN FOR THE GROUP (A): 63.0428 12.7644 130.4459 REMARK 3 T TENSOR REMARK 3 T11: 0.6679 T22: 0.2350 REMARK 3 T33: 0.4981 T12: 0.1652 REMARK 3 T13: 0.0604 T23: 0.0176 REMARK 3 L TENSOR REMARK 3 L11: 4.0807 L22: 1.2609 REMARK 3 L33: 3.6172 L12: -0.1330 REMARK 3 L13: 2.0508 L23: 0.6519 REMARK 3 S TENSOR REMARK 3 S11: -0.1863 S12: -0.1473 S13: -0.0560 REMARK 3 S21: 0.0511 S22: -0.0455 S23: 0.1028 REMARK 3 S31: -0.3311 S32: -0.0216 S33: 0.2451 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6IP0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1300009659. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JAN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2824 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45790 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 19.30 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 36.1500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 19.40 REMARK 200 R MERGE FOR SHELL (I) : 0.65100 REMARK 200 R SYM FOR SHELL (I) : 0.65100 REMARK 200 FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 75.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES, PH 6.5, 8% DIOXANE, AND 1.6M REMARK 280 AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+2/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 154.34667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 77.17333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 154.34667 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 77.17333 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 154.34667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 77.17333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 154.34667 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 77.17333 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 S SO4 A 612 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 89 REMARK 465 GLU A 90 REMARK 465 THR A 91 REMARK 465 ASP A 92 REMARK 465 LEU A 565 REMARK 465 ILE A 566 REMARK 465 THR A 567 REMARK 465 THR A 568 REMARK 465 ASP A 569 REMARK 465 GLU A 570 REMARK 465 ASP A 571 REMARK 465 LEU A 572 REMARK 465 TYR A 573 REMARK 465 LYS A 574 REMARK 465 TYR A 575 REMARK 465 PRO A 576 REMARK 465 SER A 577 REMARK 465 SER A 578 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLU A 114 -139.32 49.36 REMARK 500 CYS A 203 -12.06 70.77 REMARK 500 CYS A 223 16.92 -148.50 REMARK 500 ASP A 234 29.13 46.32 REMARK 500 ASP A 344 -127.94 59.67 REMARK 500 TYR A 517 -2.31 79.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 602 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 293 NE2 REMARK 620 2 GLU A 295 OE1 107.4 REMARK 620 3 HIS A 388 NE2 78.8 78.0 REMARK 620 4 AKG A 601 O1 178.8 73.8 101.6 REMARK 620 5 AKG A 601 O5 97.5 155.1 109.4 81.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 603 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 500 SG REMARK 620 2 CYS A 503 SG 112.0 REMARK 620 3 CYS A 522 SG 115.6 108.0 REMARK 620 4 HIS A 525 NE2 98.6 116.4 106.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 604 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 514 SG REMARK 620 2 CYS A 516 SG 109.4 REMARK 620 3 HIS A 519 ND1 104.7 101.1 REMARK 620 4 CYS A 534 SG 102.9 123.9 113.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AKG A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 608 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 609 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 610 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 611 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 612 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 613 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 614 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 615 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 616 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 617 DBREF1 6IP0 A 90 578 UNP A0A1P8BAS6_ARATH DBREF2 6IP0 A A0A1P8BAS6 90 578 SEQADV 6IP0 SER A 89 UNP A0A1P8BAS EXPRESSION TAG SEQRES 1 A 490 SER GLU THR ASP ASP LEU LYS TRP THR GLU ARG LEU PRO SEQRES 2 A 490 GLU CYS PRO VAL TYR ARG PRO THR LYS GLU GLU PHE GLU SEQRES 3 A 490 ASP PRO LEU THR TYR LEU GLN LYS ILE PHE PRO GLU ALA SEQRES 4 A 490 SER LYS TYR GLY ILE CYS LYS ILE VAL SER PRO LEU THR SEQRES 5 A 490 ALA THR VAL PRO ALA GLY ALA VAL LEU MET LYS GLU LYS SEQRES 6 A 490 SER ASN PHE LYS PHE THR THR ARG VAL GLN PRO LEU ARG SEQRES 7 A 490 LEU ALA GLU TRP ASP SER ASP ASP LYS VAL THR PHE PHE SEQRES 8 A 490 MET SER GLY ARG THR TYR THR PHE ARG ASP TYR GLU LYS SEQRES 9 A 490 MET ALA ASN LYS VAL PHE ALA ARG ARG TYR CYS SER GLY SEQRES 10 A 490 GLY SER LEU PRO ASP SER PHE LEU GLU LYS GLU PHE TRP SEQRES 11 A 490 LYS GLU ILE ALA CYS GLY LYS THR GLU THR VAL GLU TYR SEQRES 12 A 490 ALA CYS ASP VAL ASP GLY SER ALA PHE SER SER ALA PRO SEQRES 13 A 490 GLY ASP PRO LEU GLY SER SER LYS TRP ASN LEU ASN LYS SEQRES 14 A 490 VAL SER ARG LEU PRO LYS SER THR LEU ARG LEU LEU GLU SEQRES 15 A 490 THR SER ILE PRO GLY VAL THR GLU PRO MET LEU TYR ILE SEQRES 16 A 490 GLY MET LEU PHE SER MET PHE ALA TRP HIS VAL GLU ASP SEQRES 17 A 490 HIS TYR LEU TYR SER ILE ASN TYR GLN HIS CYS GLY ALA SEQRES 18 A 490 SER LYS THR TRP TYR GLY ILE PRO GLY SER ALA ALA LEU SEQRES 19 A 490 LYS PHE GLU LYS VAL VAL LYS GLU CYS VAL TYR ASN ASP SEQRES 20 A 490 ASP ILE LEU SER THR ASN GLY GLU ASP GLY ALA PHE ASP SEQRES 21 A 490 VAL LEU LEU GLY LYS THR THR ILE PHE PRO PRO LYS THR SEQRES 22 A 490 LEU LEU ASP HIS ASN VAL PRO VAL TYR LYS ALA VAL GLN SEQRES 23 A 490 LYS PRO GLY GLU PHE VAL VAL THR PHE PRO ARG ALA TYR SEQRES 24 A 490 HIS ALA GLY PHE SER HIS GLY PHE ASN CYS GLY GLU ALA SEQRES 25 A 490 VAL ASN PHE ALA MET GLY ASP TRP PHE PRO PHE GLY ALA SEQRES 26 A 490 ILE ALA SER CYS ARG TYR ALA HIS LEU ASN ARG VAL PRO SEQRES 27 A 490 LEU LEU PRO HIS GLU GLU LEU ILE CYS LYS GLU ALA MET SEQRES 28 A 490 LEU LEU ASN SER SER SER LYS SER GLU ASN LEU ASP LEU SEQRES 29 A 490 THR PRO THR GLU LEU SER GLY GLN ARG SER ILE LYS THR SEQRES 30 A 490 ALA PHE VAL HIS LEU ILE ARG PHE LEU HIS LEU ALA ARG SEQRES 31 A 490 TRP SER LEU MET LYS SER GLY LEU CYS THR GLY LEU VAL SEQRES 32 A 490 SER ASN THR TYR GLY THR ILE VAL CYS SER LEU CYS LYS SEQRES 33 A 490 ARG ASP CYS TYR LEU ALA PHE ILE ASN CYS GLU CYS TYR SEQRES 34 A 490 SER HIS PRO VAL CYS LEU ARG HIS ASP VAL LYS LYS LEU SEQRES 35 A 490 ASP LEU PRO CYS GLY THR THR HIS THR LEU TYR LEU ARG SEQRES 36 A 490 ASP ASN ILE GLU ASP MET GLU ALA ALA ALA MET LYS PHE SEQRES 37 A 490 GLU LYS GLU ASP GLY VAL SER ASP LEU ILE THR THR ASP SEQRES 38 A 490 GLU ASP LEU TYR LYS TYR PRO SER SER HET AKG A 601 10 HET NI A 602 1 HET ZN A 603 1 HET ZN A 604 1 HET SO4 A 605 5 HET SO4 A 606 5 HET SO4 A 607 5 HET SO4 A 608 5 HET SO4 A 609 5 HET SO4 A 610 5 HET SO4 A 611 5 HET SO4 A 612 5 HET SO4 A 613 5 HET SO4 A 614 5 HET SO4 A 615 5 HET SO4 A 616 5 HET SO4 A 617 5 HETNAM AKG 2-OXOGLUTARIC ACID HETNAM NI NICKEL (II) ION HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION FORMUL 2 AKG C5 H6 O5 FORMUL 3 NI NI 2+ FORMUL 4 ZN 2(ZN 2+) FORMUL 6 SO4 13(O4 S 2-) FORMUL 19 HOH *146(H2 O) HELIX 1 AA1 LYS A 95 LEU A 100 1 6 HELIX 2 AA2 THR A 109 GLU A 114 1 6 HELIX 3 AA3 ASP A 115 SER A 128 1 14 HELIX 4 AA4 PRO A 144 GLU A 152 1 9 HELIX 5 AA5 ARG A 166 TRP A 170 5 5 HELIX 6 AA6 ASP A 171 SER A 181 1 11 HELIX 7 AA7 THR A 186 CYS A 203 1 18 HELIX 8 AA8 PRO A 209 GLY A 224 1 16 HELIX 9 AA9 ASN A 254 LEU A 261 5 8 HELIX 10 AB1 SER A 264 LEU A 269 5 6 HELIX 11 AB2 GLU A 295 LEU A 299 5 5 HELIX 12 AB3 PRO A 317 SER A 319 5 3 HELIX 13 AB4 ALA A 320 ASN A 334 1 15 HELIX 14 AB5 ALA A 346 GLY A 352 1 7 HELIX 15 AB6 PRO A 358 ASP A 364 1 7 HELIX 16 AB7 MET A 405 ASP A 407 5 3 HELIX 17 AB8 TRP A 408 LEU A 422 1 15 HELIX 18 AB9 PRO A 429 SER A 444 1 16 HELIX 19 AC1 LYS A 446 LEU A 452 1 7 HELIX 20 AC2 THR A 453 GLY A 485 1 33 HELIX 21 AC3 ASP A 526 LEU A 530 5 5 HELIX 22 AC4 ASN A 545 LYS A 558 1 14 SHEET 1 AA1 8 VAL A 105 TYR A 106 0 SHEET 2 AA1 8 ILE A 132 VAL A 136 1 O VAL A 136 N TYR A 106 SHEET 3 AA1 8 GLU A 378 THR A 382 -1 O PHE A 379 N ILE A 135 SHEET 4 AA1 8 TYR A 300 GLY A 308 -1 N SER A 301 O THR A 382 SHEET 5 AA1 8 ASN A 396 PHE A 403 -1 O GLU A 399 N TYR A 304 SHEET 6 AA1 8 MET A 280 GLY A 284 -1 N TYR A 282 O GLY A 398 SHEET 7 AA1 8 THR A 228 VAL A 235 -1 N VAL A 235 O LEU A 281 SHEET 8 AA1 8 ARG A 161 PRO A 164 -1 N ARG A 161 O TYR A 231 SHEET 1 AA2 2 PHE A 158 THR A 159 0 SHEET 2 AA2 2 THR A 184 TYR A 185 -1 O TYR A 185 N PHE A 158 SHEET 1 AA3 4 MET A 289 HIS A 293 0 SHEET 2 AA3 4 HIS A 388 SER A 392 -1 O GLY A 390 N PHE A 290 SHEET 3 AA3 4 LYS A 311 GLY A 315 -1 N TYR A 314 O ALA A 389 SHEET 4 AA3 4 TYR A 370 GLN A 374 -1 O ALA A 372 N TRP A 313 SHEET 1 AA4 3 GLY A 489 ASN A 493 0 SHEET 2 AA4 3 THR A 539 ARG A 543 1 O LEU A 540 N GLY A 489 SHEET 3 AA4 3 ALA A 510 ASN A 513 -1 N PHE A 511 O TYR A 541 SHEET 1 AA5 2 ILE A 498 VAL A 499 0 SHEET 2 AA5 2 ASP A 506 CYS A 507 -1 O CYS A 507 N ILE A 498 LINK NE2 HIS A 293 NI NI A 602 1555 1555 2.15 LINK OE1 GLU A 295 NI NI A 602 1555 1555 2.07 LINK NE2 HIS A 388 NI NI A 602 1555 1555 2.06 LINK SG CYS A 500 ZN ZN A 603 1555 1555 2.41 LINK SG CYS A 503 ZN ZN A 603 1555 1555 2.41 LINK SG CYS A 514 ZN ZN A 604 1555 1555 2.36 LINK SG CYS A 516 ZN ZN A 604 1555 1555 2.34 LINK ND1 HIS A 519 ZN ZN A 604 1555 1555 2.02 LINK SG CYS A 522 ZN ZN A 603 1555 1555 2.36 LINK NE2 HIS A 525 ZN ZN A 603 1555 1555 2.17 LINK SG CYS A 534 ZN ZN A 604 1555 1555 2.32 LINK O1 AKG A 601 NI NI A 602 1555 1555 2.08 LINK O5 AKG A 601 NI NI A 602 1555 1555 2.06 SITE 1 AC1 12 TYR A 282 PHE A 290 HIS A 293 GLU A 295 SITE 2 AC1 12 SER A 301 ASN A 303 LYS A 311 TRP A 313 SITE 3 AC1 12 HIS A 388 NI A 602 SO4 A 615 HOH A 703 SITE 1 AC2 5 HIS A 293 GLU A 295 HIS A 388 AKG A 601 SITE 2 AC2 5 HOH A 703 SITE 1 AC3 4 CYS A 500 CYS A 503 CYS A 522 HIS A 525 SITE 1 AC4 4 CYS A 514 CYS A 516 HIS A 519 CYS A 534 SITE 1 AC5 5 THR A 488 LEU A 542 ARG A 543 ASP A 544 SITE 2 AC5 5 HOH A 701 SITE 1 AC6 4 PRO A 426 LEU A 427 LEU A 428 PRO A 429 SITE 1 AC7 5 TYR A 495 PHE A 511 ASN A 513 TYR A 517 SITE 2 AC7 5 HOH A 753 SITE 1 AC8 5 ARG A 188 ALA A 199 ARG A 200 CYS A 203 SITE 2 AC8 5 SO4 A 609 SITE 1 AC9 7 ARG A 188 LYS A 192 LYS A 196 ARG A 200 SITE 2 AC9 7 SO4 A 608 SO4 A 612 HOH A 786 SITE 1 AD1 4 ARG A 188 LYS A 192 ASN A 195 LYS A 196 SITE 1 AD2 3 LYS A 153 SER A 154 HOH A 714 SITE 1 AD3 4 LYS A 192 LYS A 196 TYR A 517 SO4 A 609 SITE 1 AD4 2 PHE A 411 ILE A 414 SITE 1 AD5 6 LYS A 157 THR A 184 THR A 186 TYR A 495 SITE 2 AD5 6 GLY A 496 HOH A 800 SITE 1 AD6 8 TYR A 231 ILE A 283 GLY A 284 SER A 288 SITE 2 AD6 8 MET A 289 LYS A 311 SER A 392 AKG A 601 SITE 1 AD7 3 ALA A 346 PHE A 347 ARG A 418 SITE 1 AD8 2 HIS A 525 ASP A 526 CRYST1 129.670 129.670 231.520 90.00 90.00 120.00 P 62 2 2 12 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.007712 0.004452 0.000000 0.00000 SCALE2 0.000000 0.008905 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004319 0.00000